Variant report

Variant	rs4979163
Chromosome Location	chr9:115608188-115608189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115608067..115608649-chr9:115665121..115665685,2	MCF-7	breast:
2	chr9:115606178..115608888-chr9:115665655..115667772,2	K562	blood:
3	chr9:115607981..115610113-chr9:115651782..115654095,2	MCF-7	breast:
4	chr9:115607502..115609208-chr9:115615429..115617354,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119457	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10115576	0.81[GIH][hapmap]
rs10117017	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10117709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10122712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10124939	0.81[GIH][hapmap]
rs10481638	0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10481671	0.81[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs10732374	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10733595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10733596	0.93[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10733597	0.93[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10739371	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10739375	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10759587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10759588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759589	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs10759591	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10759592	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10759593	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10759596	0.93[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10759597	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10759598	0.93[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10759599	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs10759600	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs10759601	0.93[CEU][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10817391	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10817392	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10817393	0.84[JPT][hapmap]
rs10817394	0.86[JPT][hapmap]
rs10817395	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10817396	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817397	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10817398	0.93[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10817399	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs10817400	0.92[CEU][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10817401	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10817402	0.81[CEU][hapmap]
rs10981513	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10981515	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10981516	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10981519	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10981520	0.84[JPT][hapmap]
rs10981521	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10981522	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10981523	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11791125	0.96[ASN][1000 genomes]
rs11793016	0.96[ASN][1000 genomes]
rs1418408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1475292	0.93[CEU][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1475293	0.81[GIH][hapmap]
rs1539340	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1539341	0.87[GIH][hapmap];0.82[ASN][1000 genomes]
rs1539342	0.93[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1539345	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1891403	0.81[GIH][hapmap]
rs1970527	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1970528	0.93[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2000204	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2051017	0.80[CEU][hapmap]
rs2096186	0.85[ASN][1000 genomes]
rs2096187	0.81[ASN][1000 genomes]
rs2153839	0.89[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2185767	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2645988	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2676622	0.80[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs2796024	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2798315	0.80[CEU][hapmap]
rs4276760	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4366151	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4367629	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4978504	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4978511	0.81[GIH][hapmap]
rs4979158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4979162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4979164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979166	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.93[ASN][1000 genomes]
rs4979167	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4979168	0.93[CEU][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57546880	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs57672123	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59645636	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60989307	0.96[ASN][1000 genomes]
rs61626147	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6477960	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6477961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7030460	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7032401	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7032763	0.81[CEU][hapmap]
rs7039715	0.84[AFR][1000 genomes]
rs7856199	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7871799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs787271	0.81[GIH][hapmap]
rs787274	0.81[GIH][hapmap]
rs787280	0.81[GIH][hapmap]
rs787282	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs787283	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs787288	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs787295	0.81[GIH][hapmap]
rs787297	0.81[GIH][hapmap]
rs7873644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs870078	0.89[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs883462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs912661	0.81[CEU][hapmap];0.82[ASN][1000 genomes]
rs9299210	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9299211	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9299212	0.93[CEU][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs999018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv2422302	chr9:115550339-115656433	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv2757351	chr9:115600623-115632898	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv8560	chr9:115604643-115608912	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115570600-115608400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:115577600-115630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr9:115580200-115608400	Weak transcription	Fetal Kidney	kidney
4	chr9:115582200-115608600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:115582400-115608600	Weak transcription	NHLF	lung
6	chr9:115582400-115609000	Weak transcription	NHDF-Ad	bronchial
7	chr9:115582400-115630000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr9:115584400-115608800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:115591400-115623200	Weak transcription	Fetal Heart	heart
10	chr9:115593200-115611000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr9:115594200-115610800	Weak transcription	Esophagus	oesophagus
12	chr9:115594200-115616000	Weak transcription	Small Intestine	intestine
13	chr9:115594200-115620400	Weak transcription	Thymus	Thymus
14	chr9:115594200-115634400	Weak transcription	NH-A	brain
15	chr9:115594400-115608600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:115594400-115626800	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:115596400-115613600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr9:115598600-115615200	Weak transcription	Psoas Muscle	Psoas
19	chr9:115598800-115608400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr9:115598800-115608800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr9:115598800-115610600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:115598800-115613200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr9:115599000-115623200	Weak transcription	Right Ventricle	heart
24	chr9:115599400-115608800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:115599400-115609000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:115599400-115610600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:115599400-115612000	Weak transcription	Pancreas	Pancrea
28	chr9:115599400-115612800	Weak transcription	Placenta	Placenta
29	chr9:115599400-115613000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:115599400-115615200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:115599400-115623600	Weak transcription	Right Atrium	heart
32	chr9:115599400-115625200	Weak transcription	Colonic Mucosa	Colon
33	chr9:115600800-115608600	Weak transcription	HSMM	muscle
34	chr9:115601000-115610600	Weak transcription	Spleen	Spleen
35	chr9:115601000-115612400	Weak transcription	Aorta	Aorta
36	chr9:115601200-115641200	Weak transcription	Fetal Brain Male	brain
37	chr9:115601400-115612800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr9:115601600-115610600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:115601600-115620600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:115601800-115613000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr9:115602000-115620600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:115602200-115609000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:115602200-115613200	Weak transcription	Left Ventricle	heart
44	chr9:115602400-115610800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr9:115602400-115611600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr9:115602400-115612400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr9:115602400-115613000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr9:115602400-115613200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr9:115602400-115613400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:115602600-115610600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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